Research Outputs (School of Animal, Plant and Environmental Sciences)

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    A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa
    (Public Library of Science, 2018-03) Geldenhuys, M.; Mortlock, M.; Weyer, J.; Bezuidt, O.; Seamark, E.C.J; Kearney, T.
    Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.
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    Carnivore conservation needs evidence based livestock protection
    (Public Library of Science, 2018-09) van Eeden, L.M.; Eklund, A.; Miller, J.R.B.; López-Bao, J.V; Chapron, G.; Cejtin, M.R.; McManus, J.
    Carnivore predation on livestock often leads people to retaliate. Persecution by humans has contributed strongly to global endangerment of carnivores. Preventing livestock losses would help to achieve three goals common to many human societies: preserve nature, protect animal welfare, and safeguard human livelihoods. Between 2016 and 2018, four independent reviews evaluated >40 years of research on lethal and nonlethal interventions for reducing predation on livestock. From 114 studies, we find a striking conclusion: scarce quantitative comparisons of interventions and scarce comparisons against experimental controls preclude strong inference about the effectiveness of methods. For wise investment of public resources in protecting livestock and carnivores, evidence of effectiveness should be a prerequisite to policy making or large-scale funding of any method or, at a minimum, should be measured during implementation. An appropriate evidence base is needed, and we recommend a coalition of scientists and managers be formed to establish and encourage use of consistent standards in future experimental evaluations.
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    Chiefs in a Democracy: A Case Study of the 'New' Systems of Regulating Firewood Harvesting in Post-Apartheid South Africa
    (MDPI, 2018-03) Findlay, S.J.; Twine, W.C.
    Much of the international commons literature reveals a decreased functioning of local traditional institutions that regulate natural resource harvesting. In South Africa, it is believed that the creation of new democratic structures at the end of Apartheid has contributed significantly to the deterioration in traditional resource regulation and this in turn has led to the extensive resource degradation seen in parts of the country. Many of these assertions, though, remain anecdotal in nature. Given the high reliance by rural households on natural resources, and the serious negative implications that over-use has on livelihood security, understanding how well or poorly such commons are regulated is key to ensuring the sustainability of such resource-dependent populations. The aim of this study was therefore to examine systems of resource governance, focusing specifically on firewood, and to determine the roles of traditional and democratically elected community leaders in six rural villages spanning two chieftaincies in Bushbuckridge, South Africa. In each study village, five local leaders were interviewed and five community focus groups were conducted. Results indicate that most parties still regard the Chief as the ultimate authority for regulating firewood harvesting. However, overall firewood management appears weak, at best, across the region. Although some authors attribute this to community confusion over the roles of local leaders in a new democracy, we provide evidence that other socio-political factors, including political expediency, may be driving the increasingly relaxed implementation of these firewood management systems. With resource dependence remaining a vital contributor to livelihood security across the developing world and with many rural communities facing increasing strain under local resource depletion, these findings shed new light on the complex social dynamics underlying the widely reported weakening of traditional institutions in South Africa. In so doing, it offers insights into local firewood governance that can be used to combat these challenges and thereby reduce regional social and ecological vulnerability being experienced in communal landscapes across the region.
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    Variation by Geographic Scale in the Migration-Environment Association: Evidence from Rural South Africa
    (Federal Institute for Population Research, 2017) Hunter, L.M.; Leyk, S.; Maclaurin, G.J.; Nawrotzki, R.; Twine, W.; Erasmus, B.F.N.; Collinson, M.
    Scholarly understanding of human migration’s environmental dimensions has greatly advanced in the past several years, motivated in large part by public and policy dialogue around “climate migrants”. The research presented here advances current demographic scholarship both through its substantive interpretations and conclusions, as well as its methodological approach. We examine temporary rural South African outmigration as related to household-level availability of proximate natural resources. Such “natural capital” is central to livelihoods in the region, both for sustenance and as materials for market-bound products. The results demonstrate that the association between local environmental resource availability and outmigration is, in general, positive: households with higher levels of proximate natural capital are more likely to engage in temporary migration. In this way, the general findings support the “environmental surplus” hypothesis that resource security provides a foundation from which households can invest in migration as a livelihood strategy. Such insight stands in contrast to popular dialogue, which tends to view migration as a last resort undertaken only by the most vulnerable households. As another important insight, our findings demonstrate important spatial variation, complicating attempts to generalize migration-environment findings across spatial scales. In our rural South African study site, the positive association between migration and proximate resources is actually highly localized, varying from strongly positive in some villages to strongly negative in others. We explore the socio-demographic factors underlying this “operational scale sensitivity”. The cross-scale methodologies applied here offer nuance unavailable within more commonly used global regression models, although also introducing complexity that complicates story-telling and inhibits generalizability.
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    Evaluating invasion risk for freshwater fishes in South Africa
    (National Botanical Institute/AOSIS, 2017-03) Marr, S.M.; Ellender, B.R.; Woodford, D.J.; Alexander, M.E.; Wasserman, R.J.; Ivey, P.; Zengeya, T.; Weyl, O.L.F.
    South Africa, as a signatory of the Convention on Biological Diversity, has an obligation to identify, prioritise and manage invasive species and their introduction pathways. However, this requires knowledge of the introduction pathways, factors influencing establishment success, invasive potential, current distributions and ecological impacts. Objectives: To evaluate the Fish Invasiveness Screening Kit (FISK) to predict the invasion risk posed by fish species proposed for introduction into South Africa. Method: FISK assessments were compiled for species whose invasion status in South Africa was known. A Receiver operating characteristic (ROC) analysis was conducted to calibrate the FISK for South Africa. The calibrated FISK was used to evaluate the risk that three species recently proposed for importation for aquaculture could become invasive in South Africa. Results: A FISK score of 14 was identified as the threshold to delineate between species that could become invasive in South Africa and those that are unlikely to become invasive. Of the three species evaluated, Silurus glanis had a high risk of becoming invasive in South Africa, Lates calcarifer was likely to be invasive and Oncorhynchus tshawytscha was unlikely to be invasive in South Africa. Conclusion: FISK was demonstrated to be a useful risk assessment tool to evaluate the invasion risk posed by species proposed for use in aquaculture. For the large number of fish imported for the pet trade, a rapid screening assessment to flag potentially high risk species was recommended prior to a full FISK assessment for flagged species.
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    Application of maghemite nanoparticles as sorbents for the removal of Cu(II), Mn(II) and U(VI) ions from aqueous solution in acid mine drainage conditions.
    (Springer, 2016-06) Etale, A.; Tutu, H.; Drake, D.C.
    The adsorptive removal of Cu(II), Mn(II) and U(VI) by maghemite nanoparticles (NPs) was investigated under acid mine drainage (AMD) conditions to assess NP potential for remediating AMD-contaminated water. The effects of time, NP and metal concentration, as well as manganese and sulphate ions were quantified at pH 3. Adsorption of all three ions was rapid, and equilibrium was attained in 5 min or less. 56 % of Cu, 53 % of Mn and 49 % of U were adsorbed. In addition, adsorption efficiencies were enhanced by >= 10 % in the presence of manganese and sulphate ions, although Cu sorption was reduced in 1: 2 Cu-to-Mn solutions. Adsorption also increased with pH: 86 % Cu, 62 % Mn and 77 % U were removed from solution at pH 9 and increasing initial metal concentrations. Increasing NP concentrations did not, however, always increase metal removal. Kinetics data were best described by a pseudo-second-order model, implying chemisorption, while isotherm data were better fitted by the Freundlich model. Metal removal by NPs was then tested in AMD-contaminated surface and ground water. Removal efficiencies of up to 46 % for Cu and 54 % for Mn in surface water and 8 % for Cu and 50 % for Mn in ground water were achieved, confirming that maghemite NPs can be applied for the removal of these ions from AMD-contaminated waters. Notably, whereas sulphates may increase adsorption efficiencies, high Mn concentrations in AMD will likely inhibit Cu sorption.